calc_centralize_matrix | Function to centralize a matrix X by column |
calc_EG | Function to calculate the conditional expected genotype... |
calc_EG_general | More general function to calculate the conditional expected... |
calc_EG_Var | Function to calculate the variance of conditional expected... |
calc_EG_Var_general | Function to calculate the variance of conditional expected... |
calc_EM | Function to use EM algorithm to estimate the genotype... |
calc_Mr | Function to calcualte likelihood P(D|G) for simulating data,... |
calc_pobs_ndepth | Function to calculate the likelihood matrix P(D|G) given a... |
calc_psingle | Function to compute the genotype likelihood of a read given... |
calc_robust_Var | Function to calcualte the robust variance of E(Gij|Dij) for... |
calc_score_test | Function to calculate the score test for given expected... |
calc_score_test1 | clac_score_test1 calculates the score test for given expected... |
calc_ScoreV | calc_ScoreV gets score vector S for nsnp number of rare... |
calc_ScoreV_likely | calc_ScoreV_likely: Get Variance of vector S by likelihood... |
calc_ScoreV_regVar | calc_ScoreV_regVar: Get Variance of vector S by regular... |
calc_ScoreV_RVS | calc_ScoreV_RVS calculates variance of vector S by RVS using... |
calc_simu_exp | Function to calculate expected genotype data for simuation... |
check_hom_matrix | Function to remove the homozygosity of a rare SNP in case or... |
clist | clist can combine two lists with the same structure. |
combine_twogeno | Function to combine two sets of ped pairs for two samples |
common_coord | Function to find the variants presenting in two datasets. |
convert | convert two columns of a variant from ped file into additive... |
cor.X.function | Function to edit the correlation matrix of expected genotype... |
filter_by_miss | Function to filter out variants by missing rate p |
filter_genocall | Function to filter out variants in the genotype hard call... |
filter_VCF_SNPs | Function to filter variants in VCF files based on column 2... |
generate_seq_1ind | Generate sequence data for one indiviudal with read depth rd... |
generate_seqdata_1var | Generate sequence data for ncase and ncontrol indiviudal at... |
generate_seqdata_OR | Function to simulate data for one variant by given parameters |
generate_seqdata_OR1 | Function to simulate data for one variant by given parameters |
geno_add_2pheno | Function to add the phenotype in the 6th column of the... |
geno_process | Function to deal with genotype hard call files in additive... |
get_allele_frq | Function to calculate the allele frequency from additive... |
get_exp_geno | Function to generates the expected probabilities of the... |
get_exp_MAF | Function to calculate the minor allele frequency (MAF) from... |
get_IDs | Function to seprates the case and control IDs. |
get_likelihood_vcf | Function to get Likelihoods for all possible genotypes given... |
get_lsingle_vcf | Function to parse Phred-scaled likelihoods |
minor_allele | Function to find the minor allele in the whole sample |
odds.2.probs | Function to calculate the probability from given odds |
ped_2_additive | Function to combine two ped files for case and controls and... |
rbindlist | rbindlist can rbind combine two lists with the same... |
regScore_perm | Use regular Score/Trend test for association for given... |
regScore_Rao | Use regular Score/Trend test for association for given... |
regScore_rare | It calls functions... |
regScore_rare1 | It calls functions... |
reset_minor_additive | Function to reset the additive coding genotype into nubmer of... |
RVS_asy | RVS using asymptotic distribution for score test statistic |
RVS_btrap | use RVS to test associaton by bootrtrap, given phenotype (Y),... |
RVS_rare | It calls functions... |
RVS_rare1 | It calls functions... |
RVS_rare2 | It calls functions... |
sample_bootstrap | Function to bootstrap sampling |
seq_call | Function to produce a sequencing read at one locus with... |
seqdata_nvar | Generate sequence data for nsnp variants |
seq_eg_freq | use the simulated data to calculate the expected genotype... |
sim.corr.binary.data | Function to simulate the correlated binary data with given... |
snp_true_2T | Function to change all TRUE genotype into T |
subset_ind | Function to take a subset the samples from a larger genotype... |
subset_snp | Function to extract the genotype columns for chosen variants... |
test_Calpha | Function to obtain p-value by Calpha method (quadratic test)... |
test_CAST | Function to obtain p-value by CAST method (linear test) for J... |
test_Hotelling | Function to obtain pvalue by Hotelling test for J number of... |
vcf_process | the main function to call the VCF file and return the... |
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